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sites.yml
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sites:
- name: "ImageJ"
id: "ImageJ"
url: "https://update.imagej.net/"
description: >-
Base update site for [ImageJ2](https://imagej.net/ImageJ2). No need
to add this to your list of update sites; it is already included.
maintainers:
- "[ImageJ developers](https://imagej.net/Contributors)"
- name: "Fiji"
id: "Fiji"
url: "https://update.fiji.sc/"
description: >-
Base update site for [Fiji](https://imagej.net/Fiji) and
[core Fiji plugins](https://imagej.net/Category:Plugins).
If you [downloaded Fiji directly](https://imagej.net/Downloads),
it is already included.
maintainers:
- "[Fiji developers](https://imagej.net/Contributors)"
- name: "Fiji-Legacy"
id: "Fiji-Legacy"
url: "https://sites.imagej.net/Fiji-Legacy/"
description: >-
Restores old Fiji plugins which never made the transition to Maven, as
well as obsolete libraries no longer used by current Fiji installations.
maintainers:
- "UNSUPPORTED"
- name: "Java-8"
id: "Java-8"
url: "https://sites.imagej.net/Java-8/"
description: >-
Temporary base update site for [ImageJ2](https://imagej.net/ImageJ2) and
[Fiji](https://imagej.net/Fiji) components as everything migrates to Java
8. __Will not work with Java 6 or 7.__
See [this page](https://imagej.net/Java_8) for details.
maintainers:
- "[ImageJ and Fiji developers](https://imagej.net/Contributors)"
- name: "2015-Conference"
id: "2015-Conference"
url: "https://sites.imagej.net/2015-Conference/"
description: >-
A collection of plugins highlighting the latest features of ImageJ. As
seen in [Wayne Rasband](https://imagej.net/Wayne_Rasband)'s
[opening talk](https://vimeo.com/140929691) at the
[2015 conference](https://imagej.net/Conference_2015)!
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "3D ImageJ Suite"
id: "Tboudier"
url: "https://sites.imagej.net/Tboudier/"
description: >-
A [suite of plugins](https://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start)
providing enhanced 3D capabilities in ImageJ.
maintainers:
- "[Thomas Boudier](https://imagej.net/User:Tboudier)"
- name: "3Dscript"
id: "3Dscript"
url: "https://romulus.oice.uni-erlangen.de/updatesite/"
description: >-
[3Dscript](https://imagej.net/3Dscript) is a plugin animating 3D/4D microscopy data using a natural-language-based syntax.
maintainers:
- "[Benjamin Schmid](https://imagej.net/User:Bene)"
- name: "ActogramJ"
id: "ActogramJ"
url: "https://romulus.oice.uni-erlangen.de/imagej/updatesites/ActogramJ/"
description: >-
[ActogramJ](https://bene51.github.io/ActogramJ) is a plugin for analyzing actograms.
maintainers:
- "[Benjamin Schmid](https://imagej.net/User:Bene)"
- name: "AIC Janelia - Course"
id: "AICjanelia-course"
url: "https://sites.imagej.net/AICjanelia-course/"
description: >-
A collection of plugins and macros for students of the Advanced Imaging
Center (AIC) Fiji Course.
maintainers:
- "[AIC Janelia](https://imagej.net/User:Aicjanelia)"
- name: "Angiogenesis"
id: "Angiogenesis"
url: "https://sites.imagej.net/Angiogenesis/"
description: >-
A plugin to quantify angiogenic sprout morphology.
maintainers:
- "[Jan Eglinger](https://imagej.net/User:Eglinger)"
- name: "AngioTool"
id: "AngioTool"
url: "https://sites.imagej.net/AngioTool/"
description: >-
The [AngioTool](https://ccrod.cancer.gov/confluence/display/ROB2/Home)
software converted to a Fiji plugin.
maintainers:
- "[Jan Eglinger](https://imagej.net/User:Eglinger)"
- name: "Archipelago"
id: "Lindsey"
url: "https://sites.imagej.net/Lindsey/"
description: >-
A set of plugins that allow Fiji to be run in parallel on a cluster.
Currently,
[Trainable Weka Segmentation](https://imagej.net/Trainable_Weka_Segmentation)
and [Elastic Alignment](https://imagej.net/Elastic_Alignment_and_Montage)
are accelerated in this way.
maintainers:
- "[Larry Lindsey](https://imagej.net/User:Lindsey)"
- name: "AxoNet"
id: "AxoNet"
url: "https://sites.imagej.net/AxoNet/"
description: >-
An implementation of the AxoNet tool which can be used to count axons in
light micrographs of optic nerves.
maintainers:
- "[Matthew Ritch](https://imagej.net/User:Mritch3)"
- name: "BACMMAN"
id: "Ljp"
url: "https://sites.imagej.net/Ljp/"
description: >-
BACteria in Mother Machine ANalyzer: a plugin for high-throughput
analysis of multichannel mother machine data.
See [Sources](https://github.com/jeanollion/bacmman) and [Wiki](https://github.com/jeanollion/bacmman/wiki)
maintainers:
- "Jean Ollion"
- name: "BAR"
id: "Tiago"
url: "https://sites.imagej.net/Tiago/"
description: >-
[BAR](https://imagej.net/BAR) (_Broadly Applicable Routines_) is a
[GitHub-curated](https://github.com/tferr/Scripts) collection of scripts
that simplifies the daily usage of ImageJ. The collection is focused on
Data Analysis, Image Annotation and Segmentation.
maintainers:
- "[Tiago Ferreira](https://imagej.net/User:Tiago)"
- name: "BaSiC"
id: "BaSiC"
url: "https://sites.imagej.net/BaSiC/"
description: >-
[BaSiC](https://www.helmholtz-muenchen.de/icb/research/groups/quantitative-single-cell-dynamics/software/basic/index.html)
is a retrospective image correction method for optical microscopy,
available as a Fiji/ImageJ Plugin. It is based on low rank and sparse
decomposition, which corrects both shading (uneven illumination) in space
and background bleaching in time.
maintainers:
- "[Tingying Peng](mailto:[email protected])"
- name: "BIG-EPFL"
id: "BIG-EPFL"
url: "https://sites.imagej.net/BIG-EPFL/"
description: >-
ImageJ plugins from
[EPFL's Biomedical Imaging Group (BIG)](https://imagej.net/BIG).
NOT OPEN SOURCE.
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "BigStitcher"
id: "BigStitcher"
url: "https://sites.imagej.net/BigStitcher/"
description: >-
Based on the HDF5 multi-resolution datastructures of the BigDataViewer
the BigStitcher uses globally optimal registration that is capable of
aligning large multi-tile datasets with high precision and automatic
error detection within just a few minutes while at the same time allowing
for additional user interaction.
maintainers:
- "[Stephan Preibisch](https://imagej.net/User:StephanP)"
- "[David Hörl](https://imagej.net/User:Davidhoerl)"
- name: "BigVolumeViewer Demo"
id: "BigVolumeViewer"
url: "https://sites.imagej.net/BigVolumeViewer/"
description: >-
Demo of BDV volume rendering. See
[this forum post](https://forum.image.sc/t/bigvolumeviewer-tech-demo)
for getting started.
maintainers:
- "[Tobias Pietzsch](https://imagej.net/User:Pietzsch)"
- name: "Bio-Formats"
id: "Bio-Formats"
url: "https://sites.imagej.net/Bio-Formats/"
description: >-
A version of [Bio-Formats](https://imagej.net/Bio-Formats) with the
latest bugfixes from the
[development branch](https://github.com/openmicroscopy/bioformats/tree/develop).
The last SNAPSHOTS are automatically uploaded daily.
maintainers:
- "[OME development team](https://www.openmicroscopy.org)"
- name: "Biomat"
id: "Biomat"
url: "https://sites.imagej.net/Biomat/"
description: >-
Plugins for 3D image preprocessing and detection of fibres in 3D image.
maintainers:
- "[Jiri Janacek](https://imagej.net/User:Biomat)"
- name: "Biomedgroup"
id: "Biomedgroup"
url: "https://sites.imagej.net/Biomedgroup/"
description: >-
A set of plugins developed by the biomedical imaging group of the
dortmund university of applied sciences and arts:
* [Shape Filter](https://imagej.net/Shape_Filter) (Filter binary images by shape),
* [Shape Smoothing](https://imagej.net/Shape_Smoothing) (Smooth objects via Fourier descriptors),
* [Non Local Means Denoise](https://imagej.net/Non_Local_Means_Denoise) (edge preserving noise filter),
* [NanoTrackJ](https://imagej.net/NanoTrackJ) (Size characterization of freely diffusing nanoparticles by particle tracking),
* [Ridge Detection](https://imagej.net/Ridge_Detection) (Line / Ridge detection plugin).
maintainers:
- "[Thorsten Wagner](https://imagej.net/User:Twagner)"
- name: "BioVoxxel"
id: "BioVoxxel"
url: "https://sites.imagej.net/BioVoxxel/"
description: >-
A toolset providing a plugins and macros for flat-field background
corrections, image filters, color coding of shape descriptors and several
tools to process and analyze binary images such as the 'Speckle
Inspector', 'Binary Feature Extractor' and an 'Extended Particle
Analyzer' and a qualitative and quantitative evaluation tool for Fijis'
Auto Threshold methods. More information at the
[BioVoxxel Toolbox](https://imagej.net/BioVoxxel_Toolbox) page and the
[BioVoxxel web site](https://www.biovoxxel.de).
maintainers:
- "[Jan Brocher](https://imagej.net/User:BioVoxxel)"
- name: "Blind Analysis Tools"
id: "Astja"
url: "https://sites.imagej.net/Astja/"
description: >-
Tools to facilitate blind i.e., unbiased analysis of (image) data.
For more information visit the
[documentation page](https://imagej.net/Blind_Analysis_Tools).
maintainers:
- "[Astha Jaiswal](https://imagej.net/User:Astja), Holger Lorenz"
- name: "BoneJ"
id: "BoneJ"
url: "https://sites.imagej.net/BoneJ/"
description: >-
A collection tools for trabecular geometry and whole bone shape analysis.
This update site hosts the new experimental, modernized version of BoneJ
that works with the latest Fiji. Enabling the update site creates the
menu entries Plugins > BoneJ. The pQCT tools are now hosted on their own
update site (see below).
maintainers:
- "[Michael Doube](https://imagej.net/User:Michaeldoube)"
- "[Alessandro Felder](https://imagej.net/User:Alessandrofelder)"
- name: "CALM"
id: "CALM"
url: "https://sites.imagej.net/CALM/"
description: >-
Plugins from the Crick Advanced Light Microscopy Facility at
[The Francis Crick Institute](https://www.crick.ac.uk).
maintainers:
- "[David Barry](mailto:[email protected])"
- name: "CAMDU"
id: "CAMDU"
url: "https://sites.imagej.net/CAMDU/"
description: >-
Plugins from the
[Computing and Advanced Microscopy Development Unit](https://www.warwick.ac.uk/camdu)
at the [University of Warwick](https://www.warwick.ac.uk).
maintainers:
- "[Erick Martins Ratamero](mailto:[email protected])"
- name: "CellTrackingChallenge"
id: "Ulman"
url: "https://sites.imagej.net/Ulman/"
description: >-
Implementation of measures and front-end plugins used in and related to
the [Cell Tracking Challenge](http://www.celltrackingchallenge.net).
maintainers:
- "[Vladimír Ulman](mailto:[email protected])"
- name: "CIP"
id: "CIP"
url: "https://sites.imagej.net/CIP/"
description: >-
[An image procesing toolbox focused on scripting](https://imagej.net/CIP).
maintainers:
- "[Benoit Lombardot](https://imagej.net/User:Benoit)"
- name: "CircleSkinner"
id: "CircleSkinner"
url: "https://sites.imagej.net/CircleSkinner/"
description: >-
A Fiji plugin for the automated detection and quantification of circular
structures in images.
maintainers:
- "[Jean-Yves Tinevez](https://imagej.net/User:JeanYvesTinevez)"
- name: "clij"
id: "clij"
url: "https://sites.imagej.net/clij/"
description: >-
GPU-acceleration for ImageJ.
See [https://clij.github.io/](https://clij.github.io/)
maintainers:
- "[Robert Haase](https://imagej.net/User:Haesleinhuepf)"
- name: "clij2"
id: "clij2"
url: "https://sites.imagej.net/clij2/"
description: >-
Experimental update site / incubator for the future release of clij2.
See [https://clij.github.io/clij-advanced-filters](https://clij.github.io/clij-advanced-filters)
maintainers:
- "[Robert Haase](https://imagej.net/User:Haesleinhuepf)"
- name: "ClearVolume"
id: "ClearVolume"
url: "https://sites.imagej.net/ClearVolume/"
description: >-
ClearVolume is a fast 3D viewer, for more information see also the
[ClearVolume wiki](https://github.com/ClearVolume/ClearVolume/wiki).
maintainers:
- "[ClearVolume](https://imagej.net/User:ClearVolume)"
- name: "CMCI-EMBL"
id: "Miura"
url: "https://sites.imagej.net/Miura/"
description: >-
A plugin for loading sample images and misc functionality for CMCI ImageJ
course. See [CMCI course](http://cmci.embl.de/mainpages/courses).
Eventually more plugins will be added.
maintainers:
- "[Kota Miura](https://imagej.net/User:Miura)"
- name: "CMP-BIA tools"
id: "CMP-BIA"
url: "https://sites.imagej.net/CMP-BIA/"
description: >-
The development version of
[CMP-BIA tools](https://imagej.net/CMP-BIA_tools).
maintainers:
- "[Jiri Borovec](http://cmp.felk.cvut.cz/~borovji3/)"
- name: "CMTK Registration"
id: "Jefferis"
url: "https://sites.imagej.net/Jefferis/"
description: >-
CMTK Registration GUI.
maintainers:
- "[Gregory Jefferis](https://imagej.net/User:Jefferis)"
- name: "Cookbook"
id: "Cookbook"
url: "https://sites.imagej.net/Cookbook/"
description: >-
Plugins from the [Cookbook](https://imagej.net/Cookbook).
maintainers:
- "[Cookbook Team](https://imagej.net/Cookbook#Credits)"
- name: "CSBDeep"
id: "CSBDeep"
url: "https://sites.imagej.net/CSBDeep/"
description: >-
Plugins for executing pretrained CARE networks.
maintainers:
- "[Deborah Schmidt](https://imagej.net/User:Frauzufall)"
- name: "CSIM Laboratory"
id: "Acsenrafilho"
url: "https://sites.imagej.net/Acsenrafilho/"
description: >-
A set of plugins, macros and scripts developed by the CSIM (Computing in
Signal and Images in Medicine) research group. One of the methods
available are
[Anomalous Diffusion Filters](https://imagej.net/Anomalous_Diffusion_Filters),
[Noise Generator](https://imagej.net/Noise_Generator),
[MRI Perfusion](https://imagej.net/MRI_Perfusion) and the
[Sample Entropy for Images](https://imagej.net/SampEn2D).
Please, see the [CSIM group web page](https://imagej.net/CSIMLab)
to find out how the methods works and more information about us.
maintainers:
- "[Antonio Carlos da S. Senra Filho](https://imagej.net/User:Acsenrafilho)"
- name: "CWNS dense nuclei segmenter"
id: "CWNS"
url: "https://sites.imagej.net/CWNS/"
description: >-
The Fiji implementation of the CWNS dense nuclei segmenter, presented in
["Object Segmentation and Ground Truth in 3D Embryonic Imaging"](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150853),
by B. Rajasekaran et al., Plos ONE, 2016.
maintainers:
- "[Jean-Yves Tinevez](https://imagej.net/User:JeanYvesTinevez)"
- name: "DeepClas4Bio-plugins"
id: "Adines"
url: "https://sites.imagej.net/Adines/"
description: >-
Collection of plugins that use
[DeepClas4Bio API](https://github.com/adines/DeepClas4Bio) --
an API that facilitates the interoperability of bioimaging tools with
deep learning frameworks.
maintainers:
- "[Adrián Inés](mailto:[email protected])"
- name: "DHM Utilities"
id: "Sudgy"
url: "https://sites.imagej.net/Sudgy/"
description: >-
Collection of plugins for use in digital holographic microscopy, such as
hologram reconstruction, numerical propagation, and phase unwrapping.
maintainers:
- "[David Cohoe](mailto:[email protected])"
- name: "DiameterJ"
id: "DiameterJ"
url: "https://sites.imagej.net/DiameterJ/"
description: >-
Macros for quantitative analysis of nanofiber images. DiameterJ is able
to analyze any network of connecting lines (validated for SEM micrographs
of micro- and nanofibers) and produce metrics such as mean diameter,
histograms of fiber diameter, mean pore size, histogram of all pore
areas, percent porosity, etc. See [soon](coming) for more information
and the publication describing how DiameterJ works and its limitations.
maintainers:
- "[Nathan Hotaling](https://imagej.net/User:DiameterJ)"
- name: "DiversePathsJ"
id: "Vuhlmann"
url: "https://sites.imagej.net/Vuhlmann/"
description: >-
DiversePathsJ implements a dynamic programming approach for the general
task of finding diverse shortest paths between two end-points. It is not
linked to a specific biological problem and can be applied to a large
variety of images. See the [DiversePathsJ web
page](http://bigwww.epfl.ch/algorithms/diversepathsj/) for more
information.
maintainers:
- "[Virginie Uhlmann](https://imagej.net/User:Vuhlmann)"
- name: "EMBL-CBA"
id: "EMBL-CBA"
url: "https://sites.imagej.net/EMBL-CBA/"
description: >-
Collection of image analysis tools.
* Image Registration: Plugin for n-dimensional image sequence registration [Christian Tischer](mailto:[email protected])
maintainers:
- "[EMBL-CBA](mailto:[email protected])"
- name: "EpiGraph"
id: "Pedgomgal1"
url: "https://sites.imagej.net/Pedgomgal1/"
description: >-
EpiGraph: an open-source method to quantify epithelial organization.
EpiGraph is a Fiji plugin that combines computational geometry and graph
theory to measure organization in any computational or natural
tessellation image.
maintainers:
- "[Pedro J. Gómez Gálvez](mailto:[email protected])"
- "[Pablo Vicente Munuera](https://github.com/Pablo1990)"
- name: "EZFig"
id: "EZF"
url: "https://sites.imagej.net/EZF/"
description: >-
EZFig is a tool to build publication-ready scientific figures based on
ScientiFig but simpler to use. It must be used in combination with the
'Java-8' update site.
maintainers:
- "[Benoit Aigouy](mailto:[email protected])"
- name: "FAST"
id: "FAST"
url: "https://sites.imagej.net/FAST/"
description: >-
Fluorescence image AnalysiS Tool automates tasks to process a set of
single-channel fluorescence images.
maintainers:
- "[C.TURIÈS](https://imagej.net/User:C.TURIÈS)"
- name: "FFMPEG"
id: "FFMPEG"
url: "https://fiji.sc/~schindelin/ffmpeg-plugins/"
description: >-
Fiji plugins which allow reading and writing to
[FFmpeg](https://www.ffmpeg.org/)-supported formats via native bindings.
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "FibrilJ"
id: "FibrilJ"
url: "https://sites.imagej.net/FibrilJ/"
description: >-
Macros developed to measure the diameters and persistence lengths if
amyloids fibrils by AFM, EM, STM etc. iamges. It provides histogram
distribution of the average fibril diameter and average fibril
persistence length. Was validated for AFM, SEM and TEM images of Sup35NM
fibrils on mica, silicon, gold surfaces and formvar film.
maintainers:
- "Petr Sokolov"
- name: "FilamentDetector"
id: "FilamentDetector"
url: "https://sites.imagej.net/FilamentDetector/"
description: >-
A Fiji plugin that allows easy, fast and accurate detection and tracking
of biological filaments.
maintainers:
- "[Hadrien Mary](https://imagej.net/User:Hadim)"
- name: "Filopodyan"
id: "Rb7777"
url: "https://sites.imagej.net/Rb7777/"
description: >-
Filopodia dynamics analysis. See
[GitHub](https://github.com/gurdon-institute/Filopodyan) for the user
guide, source code and R scripts for downstream analysis.
maintainers:
- "Richard Butler"
- "Vasja Urbančič"
- name: "FiloQuant"
id: "FiloQuant"
url: "https://sites.imagej.net/FiloQuant/"
description: >-
[FiloQuant](https://imagej.net/User:FiloQuant) is a user friendly and
modifiable tool for automated detection and quantification of filopodia
properties such as length and density. FiloQuant can also track
filopodia.
maintainers:
- "Guillaume Jacquemet"
- "Alexandre Carisey"
- name: "FPBioimage"
id: "Fpbioimage"
url: "https://sites.imagej.net/Fpbioimage/"
description: >-
A plugin to prepare and upload data for
[Fpbioimage](https://imagej.net/Fpbioimage).
maintainers:
- "[FPBioimage](https://imagej.net/User:Fpbioimage)"
- name: "FracLac Suite"
id: "Akarperien"
url: "https://sites.imagej.net/Akarperien/"
description: >-
Fractal Analysis and Modelling tools for neuroscience and other
disciplines. __Analysis:__ <abbr title=\"Box Counting Fractal
Dimension\">D<sub>B</sub></abbr>, <abbr title=\"Fixed Grid and Sliding
Box\">lacunarity</abbr>, multifractal spectra, <abbr title=\"Local
Connected Fractal Dimension\">D<sub>LC</sub></abbr>, <abbr title=\"Mass
vs Distance Dimension\">D<sub>MvD</sub></abbr>, subscanning, and
graphical wave analysis for binary and gray scale images, with inline and
[online](https://imagej.net/plugins/fraclac/FLHelp/Introduction.htm)
theoretical and practical help. __Outputs:__ detailed analyses, raw
data, plots, colour-coding, and settings (*.fl) files. __Modelling:__
benchmark fractals, natural structures (e.g., neurons), megadata to
graphical wave images. Code in jar. See
[citations](https://imagej.net/plugins/fraclac/FLHelp/FLCitations.htm).
maintainers:
- "[A. Karperien](https://imagej.net/User:Akarperien)"
- name: "FunImageJ"
id: "FunImageJ"
url: "https://sites.imagej.net/FunImageJ/"
description: >-
Fiji plugin that provides Clojure wrappings of many commonly used
functions from ImageJ and ImgLib2. Works with SciJava scripting for
Clojure. FunImageJ scripts can be converted into standalone
ImageJ/Fiji-based programs. Code available
[on GitHub](https://github.com/kephale/fun.imagej).
maintainers:
- "[Kyle Harrington](https://imagej.net/User:Kharrington)"
- name: "Fuzzy logic and artificial neural networks image processing toolbox for ImageJ"
id: "Astartes91"
url: "https://sites.imagej.net/Astartes91/"
description: >-
Toolbox includes fuzzy edge detection plugin, fuzzy contrast enhancement
plugin and ann edge detection plugin. Source code
[on GitHub](https://github.com/astartes91/imagej-neural-fuzzy-plugins).
maintainers:
- "[Vladimir Nizamutdinov](mailto:[email protected])"
- name: "Fuzzy Set"
id: "Rerger"
url: "https://sites.imagej.net/Rerger/"
description: >-
[Fuzzy Set](https://imagej.net/User:Rerger) is an ImageJ plugin, to
transform the intensity of the image using Fuzzy Sets.
maintainers:
- "[Robert Erger](mailto:[email protected])"
- name: "GDSC"
id: "GDSC"
url: "https://sites.imagej.net/GDSC/"
description: >-
The Genome Damage and Stability Centre (GDSC) plugins are a collection of
analysis programs for microscopy images including colocalisation analysis
and peak finding (FindFoci). See
[GDSC Plugins](http://www.sussex.ac.uk/gdsc/intranet/microscopy/imagej/gdsc_plugins)
for details.
maintainers:
- "[Alex Herbert](mailto:[email protected])"
- name: "GDSC-SMLM"
id: "GDSC-SMLM"
url: "https://sites.imagej.net/GDSC-SMLM/"
description: >-
The GDSC Single Molecule Light Microscopy (SMLM) plugins provide various
tools for single molecule localisation analysis. This includes PALM,
STORM and other single molecule microscopy methods. See
[SMLM Plugins](http://www.sussex.ac.uk/gdsc/intranet/microscopy/imagej/smlm_plugins)
for details or read the
[User Manual](http://www.sussex.ac.uk/gdsc/intranet/pdfs/SMLM.pdf).
maintainers:
- "[Alex Herbert](mailto:[email protected])"
- name: "Hadim"
id: "Hadim"
url: "https://sites.imagej.net/Hadim/"
description: >-
Contains the ij2-python-lib package.
maintainers:
- "[Hadrien Mary](https://imagej.net/User:Hadim)"
- name: "HDF5"
id: "Ronneber"
url: "https://sites.imagej.net/Ronneber/"
description: >-
The HDF5 plugin allows to load and save data in HDF5 format.
For details see
[HDF5 plugin](https://lmb.informatik.uni-freiburg.de/resources/opensource/imagej_plugins/hdf5.html).
maintainers:
- "[Olaf Ronneberger](mailto:[email protected])"
- name: "HistoJ"
id: "Pathomation"
url: "https://sites.imagej.net/Pathomation/"
description: >-
Plugin to interface with
[Pathomation's digital slide viewer](https://www.pathomation.com/)
which can open Olympus VSI (.vsi), Ventana / Roche BIF (.bif),
Hamamatsu NDPI (.ndpi), 3DHistech MRXS (.mrxs),
Aperio / Leica SVS (.svs), Leica SCN (.scn), Carl Zeiss ZVI (.zvi),
Carl Zeiss CZI (.czi), Nikon ND2 (.nd2), Sakura SVSlide (.svslide).
maintainers:
- "[Pathomation](mailto:[email protected])"
- name: "Hohlbein Lab"
id: "HohlbeinLab"
url: "https://sites.imagej.net/HohlbeinLab/"
description: >-
Plugins created by the [Hohlbein Lab](https://jhohlbein.com/) (Wageningen University,
Laboratory of Biophysics). Includes ThunderSTORM with added [phasor-based
localization](https://aip.scitation.org/doi/abs/10.1063/1.5005899) for
single-molecule microscopy analysis (pSMLM-3D, Martens et al., JCP, 2018).
maintainers:
- "[Koen Martens](mailto:[email protected])"
- "[Johannes Hohlbein](mailto:[email protected])"
- name: "IamMM"
id: "IamMM"
url: "https://sites.imagej.net/IamMM/"
description: >-
[Image Synthesizer](https://imagej.net/Image_Synthesizer) (plugin to
generate images from mathematical functions and conditional statements in
a coordinate system independent from the aspect ratio or image size),
[Spheroid RGB](https://github.com/IamMM/Spheroid_RGB) (plugin to analyze
microscopy RGB images with fluorescent stained cells)
maintainers:
- "[Maximilian Maske](mailto:[email protected] Maximilian Maske)"
- name: "IBMP-CNRS"
id: "Mutterer"
url: "https://sites.imagej.net/Mutterer/"
description: >-
[FigureJ](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:figurej:start)
(easy article figure creation),
[ActionBar](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start)
(macro-based buttons bars),
[Droplet](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:droplet:start)
(drag and drop file processor), LSM Reader and LSM Toolbox moved to the
main Fiji update site,
[IJ_Ed](https://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:ij_ed:start)
(jEdit link).
maintainers:
- "[Jerome Mutterer](mailto:[email protected])"
- name: "IJ-OpenCV-plugins"
id: "IJ-OpenCV"
url: "https://sites.imagej.net/IJ-OpenCV/"
description: >-
Collection of plugins created using the
[IJ-OpenCV library](https://github.com/joheras/IJ-OpenCV) --
a library that allows the connection of ImageJ and OpenCV.
maintainers:
- "[Jónathan Heras](mailto:[email protected])"
- name: "IJPB-plugins"
id: "IJPB-plugins"
url: "https://sites.imagej.net/IJPB-plugins/"
description: >-
Collection of plugins created at the INRA-IJPB Modeling and Digital
Imaging lab to perform 2D/3D image segmentation, fast morphological
operations and geometric analysis
maintainers:
- "[Modeling and Digital Imaging lab, INRA-Versailles](https://www-ijpb.versailles.inra.fr/en/bc/equipes/modelisation-imagerie/)"
- name: "ilastik"
id: "Ilastik"
url: "https://sites.imagej.net/Ilastik/"
description: >-
Provides interoperability between Fiji and ilastik workflows
(pixel/object classification, tracking) as well as HDF5 file
export/import.
maintainers:
- "[Adrian Wolny](mailto:[email protected])"
- name: "ImageJ Latex"
id: "Yul.liuyu"
url: "https://sites.imagej.net/Yul.liuyu/"
description: >-
Add math equations to an image using Latex.
maintainers:
- "[Yu Liu](https://imagej.net/User:Yul.liuyu)"
- name: "ImageJ-ITK"
id: "ImageJ-ITK"
url: "https://sites.imagej.net/ImageJ-ITK/"
description: >-
Adds [ITK integration](https://github.com/imagej/imagej-itk) including
conversion between [ITK](http://www.simpleitk.org/) and
[ImageJ](https://github.com/imagej/imagej) images. See the
[ITK page](https://imagej.net/ITK) for more information.
maintainers:
- "[Curtis Rueden](https://imagej.net/User:Rueden)"
- name: "ImageJ-MATLAB"
id: "MATLAB"
url: "https://sites.imagej.net/MATLAB/"
description: >-
Adds support for MATLAB
[scripting](https://github.com/scijava/scripting-matlab) and converting
between MATLAB arrays and
[ImageJ](https://github.com/imagej/imagej-matlab) components. See the
[scripting tutorial](https://imagej.net/MATLAB) for more information.
maintainers:
- "[Mark Hiner](https://imagej.net/User:Hinerm)"
- name: "ImageScience"
id: "ImageScience"
url: "https://sites.imagej.net/ImageScience/"
description: >-
Base update site for all [ImageScience](https://imagej.net/ImageScience)
related ImageJ plugins.
maintainers:
- "[Erik Meijering](https://imagej.net/User:ImageScience)"
- name: "ImagingBook"
id: "ImagingBook"
url: "https://sites.imagej.net/ImagingBook/"
description: >-
Common ImageJ/Java source code for the
[Digital Imaging books](https://imagingbook.com) by
[Wilhelm Burger](https://imagej.net/User:ImagingBook) and Mark J. Burge.
This update site only provides the common "imagingbook" LIBRARY plus
required third-parts JAR files. Specific sets of demo plugins are
available for each book edition; choose ONE of the update sites listed
below. Find the online documentation and additional materials
[on the SourceForge page](https://sourceforge.net/projects/imagingbook/).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookEn1"
id: "ImagingBookEn1"
url: "https://sites.imagej.net/ImagingBookEn1/"
description: >-
ImageJ PLUGINS (only) for "Digital Image Processing – An Algorithmic
Introduction Using Java" by W. Burger & M. Burge, Springer (2008).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookEn2"
id: "ImagingBookEn2"
url: "https://sites.imagej.net/ImagingBookEn2/"
description: >-
ImageJ PLUGINS (only) for "Principles of Digital Image Processing" (Vols.
1–3) by W. Burger & M. Burge, Springer (2009–2013).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookEn3"
id: "ImagingBookEn3"
url: "https://sites.imagej.net/ImagingBookEn3/"
description: >-
ImageJ PLUGINS (only) for "Digital Image Processing – An Algorithmic
Introduction Using Java" by W. Burger & M. Burge, 2nd ed., Springer
(2016).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookDe2"
id: "ImagingBookDe2"
url: "https://sites.imagej.net/ImagingBookDe2/"
description: >-
ImageJ PLUGINS (only) for "Digitale Bildverarbeitung – Eine Einführung
mit Java und ImageJ" by W. Burger & M. Burge, Springer (2006).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingBookDe3"
id: "ImagingBookDe3"
url: "https://sites.imagej.net/ImagingBookDe3/"
description: >-
ImageJ PLUGINS (only) for "Digitale Bildverarbeitung – Eine
algorithmische Einführung mit Java" by W. Burger & M. Burge, Springer
(2015).
maintainers:
- "[Wilhelm Burger](https://imagej.net/User:ImagingBook)"
- name: "ImagingFCS"
id: "ImagingFCS"
url: "https://sites.imagej.net/ImagingFCS/"
description: >-
Imaging_FCS 1.491 is a basic ImageJ plugin to calculate and view
spatio-temporal correlation functions from 16 bit gray tiff stack files.
It was written under FIJI (ImageJ 1.51f; Java 1.8.0_102) and requires
Imagescience for statistics (simulator) and Apache Poi for file reading
and writing.
maintainers:
- "[Thorsten Wohland](http://www.dbs.nus.edu.sg/lab/BFL/imfcs_image_j_plugin.html)"
- name: "IMCF Uni Basel"
id: "UniBas-IMCF"
url: "https://sites.imagej.net/UniBas-IMCF/"
description: >-
Various plugins (most notably the Stitching-Wrapper for Olympus FluoView
OIF / OIB mosaics), macros and Action Bars, including a LUT selection bar
that lets you click on a visual representation of the LUT. Also ships the
[MultiStackRegistration](https://github.com/miura/MultiStackRegistration)
plugin (the version modified by Kota Miura that is usable from scripts).
maintainers:
- "[Niko Ehrenfeuchter](https://imagej.net/User:Ehrenfeu)"
- name: "IMOD-ZOLA"
id: "IMOD-ZOLA"
url: "https://sites.imagej.net/IMOD-ZOLA/"
description: >-
Zernike Optimized Localization Algorithm for 3D single molecule
localizations [ZOLA-3D](https://github.com/imodpasteur/ZOLA-3D)
developed in Institut Pasteur, group IMOD -- a CUDA-enabled localization
algorithm for extended PSF single-molecule localization microscopy. Paper
is under review.
maintainers:
- "[Andrey Aristov](mailto:[email protected])"
- "[Benoit Lelandais](mailto:[email protected])"
- name: "INCF test site"
id: "Dimiterpp"
url: "https://sites.imagej.net/Dimiterpp/"
description: >-
Update site for scale space filters and other INCF projects from GSOC
2014, 2015, 2016.
maintainers:
- "[Dimiter Prodanov](mailto:[email protected])"
- name: "IsletJ"
id: "IsletJ"
url: "https://sites.imagej.net/IsletJ/"
description: >-
Plugin for evaluation of microscopy images of Langerhans islets. Provides
estimate of area and count of islets, and an estimate of purity
(endocrine-to-exocrine tissue ratio).
maintainers:
- "[Jan Schier](mailto:[email protected])"
- "[Jan Švihlík](mailto:[email protected])"
- name: "JAX Eye"
id: "MarkKrebs"
url: "https://sites.imagej.net/MarkKrebs/"
description: >-
Macro for processing brightfield fundus images of the mouse eye and
plugin for averaging replicate OCT volume scans.
maintainers:
- "[Mark Krebs](mailto:[email protected])"
- name: "JOGL Canvas Deep Color / 3D"
id: "JOGLCanvas"
url: "https://sites.imagej.net/JOGLCanvas/"
description: >-
[JOGL Canvas](https://github.com/aschain/JOGL_Canvas_DC3D) is a plugin
for ImageJ1 that uses OpenGL and a graphics card to display images
rather than the ImageCanvas class, which is extended from java's canvas.
It replaces it with a [JOGL](https://jogamp.org/jogl/www/) OpenGL
GLCanvas instead. This allows 10-bit or greater color depth for
supported monitors and some modest 3D rendering.
maintainers:
- "[Aaron Schain](https://imagej.net/User:JOGLCanvas)"
- name: "Kappa"
id: "Kappa"
url: "https://sites.imagej.net/Kappa/"
description: >-
A Fiji plugin for Curvature Analysis.
maintainers:
- "[Hadrien Mary](https://imagej.net/User:Hadim)"
- name: "Lab-utility-plugins"
id: "Georgenm"
url: "https://sites.imagej.net/Georgenm/"
description: >-
A collection of plugins for file blinding, batch image conversion of
proprietary formats to tif, and other common helper functions.
Source and docs
[on GitHub](https://github.com/Macklin-Lab/imagej-microscopy-scripts).
maintainers:
- "[Nick George](mailto:[email protected])"
- name: "Labkit"
id: "Labkit"
url: "https://sites.imagej.net/Labkit/"
description: >-
An advanced plugin for labeling and automatic segmentaion of Images.
maintainers:
- "[Matthias Arzt](mailto:[email protected])"
- name: "LAG SIM"
id: "LagSIM"
url: "https://sites.imagej.net/LagSIM/"
description: >-
A plugin and set of macro tools to help with reconstructing SIM data.
This has been specifically developed for the Laser Analytics Group SIM in
the University of Cambridge - but please download and/or modify for your
own needs.
maintainers:
- "[LagSIM](https://imagej.net/User:LagSIM)"
- name: "Leiden University"
id: "Willemsejj"
url: "https://sites.imagej.net/Willemsejj/"
description: >-
At [Leiden University](https://www.universiteitleiden.nl/) we develop
user demanded plugins for general use, which could be applicable in your
experiments as well. Most questions arise from experiments done in the
[Cell Observatory](https://www.universiteitleiden.nl/en/research/research-facilities/science/cell-observatory#tab-1).
maintainers:
- "[Joost Willemse](mailto:[email protected])"
- name: "LimeSeg"
id: "LimeSeg"
url: "https://sites.imagej.net/LimeSeg/"
description: >-
Revisited active contour method for 3D segmentation.
Documentation: [LimeSeg](https://imagej.net/LimeSeg).
maintainers:
- "[Nicolas Chiaruttini](mailto:[email protected])"
- "Sarah Machado"
- name: "Lineage-Mapper"
id: "NIST-ISG-LineageMapper"
url: "https://sites.imagej.net/NIST-ISG-LineageMapper/"
description: >-
Lineage Mapper is an open-source, overlap-based cell tracking system for
time-lapse images of biological cells, colonies, and particles. Lineage
Mapper tracks objects independently of the segmentation method, detects
mitosis in confluence, separates cell clumps mistakenly segmented as a
single cell, provides accuracy and scalability even on terabyte-sized
datasets, and creates division and/or fusion lineages.
maintainers:
- "[NIST ISG](https://isg.nist.gov/deepzoomweb/resources/csmet/pages/cell_tracking/cell_tracking.html)"
- name: "LLTT"
id: "Alex-krull"
url: "https://sites.imagej.net/Alex-krull/"
description: >-
The [Low Light Tracking Tool](https://imagej.net/Low_Light_Tracking_Tool)
can be used to track low-light sub-resolution objects in microscopy
images and other applications.
maintainers:
- "[Alexander Krull](https://imagej.net/User:Alex)"
- "[Damien Ramunno-Johnson](https://imagej.net/User:Damienrj)"
- name: "LOCI"
id: "LOCI"
url: "https://sites.imagej.net/LOCI/"
description: >-
The [LOCI](https://loci.wisc.edu/software/fiji-plugins) update site for
[their Fiji plugins](https://loci.wisc.edu/software/fiji-plugins),
including
[VisBio Fiji plugins](https://loci.wisc.edu/software/visbio-fiji-plugins)